We have analyzed thirteen years (1993 to 2005) of HALOE and over two years of EOS MLS observations (September 2004 to December 2006) for QBO and annual cycle trace variations in tropical H2O, HCl, ozone, N2O, CO, HF, and CH4. We use these results to develop the theory explaining both Brewer-Dobson circulation (BDC) and QBO driven fluctuations in tropical trace gases. For H2O, BDC variations drive part of the tropopause annual forcing through annual variations in the temperature as has been shown previously. For CO, the annual variations in the BDC amplify the annual fluctuations in CO at the tropopause as has recently been shown by Randel et al (2007). In both cases, the tropopause signal is carried upward by the mean BDC. For ozone, N2O, HCl and other gases, photochemical processes force fluctuations in the trace gases to be synchronized with annual and QBO variations in the zonal mean residual vertical velocity as is shown using lag correlations.